But according to Neil Saunders, managing director of the retail consulting firm GlobalData, the grocery chain is facing a host of issues that have nothing to do with prices.

"That Whole Foods can't turn around its fortunes is, in our opinion, the result of several fundamental flaws in its business model," Saunders wrote in a note to clients. "Over the past few years, these cracks have become more pronounced, and the company has done seemingly little to correct them."

He outlined three main issues:

1. Stores are cramped and uninspiring.

"A host of older stores, especially those in cities, are plain shabby and down at heel," Saunders said. "Even newer shops, barring some flagships like the new Bryant Park location in New York City, are not particularly revolutionary or impressive. By comparison, some mainstream grocers — like Price Chopper and its new Market 32 format — are coming out with store designs that are much more creative and inspiring than Whole Foods."

2. Food quality is 'excellent,' but the taste is 'bland and dry.'

"The offering from the hot food counters is bland and dry, prepared packaged foods are hit-and-miss, and the cake and patisserie offer is often less than inspiring," he said.

Barclays

Mainstream grocers like Wegmans are dominating Whole Foods in that department, according to Saunders.

"We think that Whole Foods makes too little effort on the 'taste' front," he said. "The result is that it is trounced by a retailer like Wegmans, which devotes enormous resources to ensuring that its products are mouthwatering."

3. 'Organic and fresh' is no longer a differentiator for Whole Foods.

Traditional and discount grocers like Kroger, Aldi, and Walmart are investing heavily in expanding their organic, natural, and fresh food selections — and stealing customers from Whole Foods in droves.

In March, Barclays analyst Karen Short estimated Whole Foods had lost as many as 14 million customers in the past six quarters, and that most of them were going to Kroger instead.

"The magnitude of the traffic declines ... is staggering," Short said. "As most retailers know, once traffic has been lost, those patterns rarely reverse."

Kroger's fresh produce department. Business Insider

Kroger now devotes several aisles in its stores to organic and natural foods and offers a variety of organic meats and fresh produce. The chain's products, including those in its Simple Truth line of organic goods, are about 15% cheaper on average than items at Whole Foods, according to a 2016 study.

Kroger's sales of organic and natural food totaled $16 billion in the past year, compared with $15.8 billion at Whole Foods, according to Barclays.

Whole Foods CEO John Mackey recently acknowledged the increasing threat from conventional grocers but did not specifically mention Kroger.

"The more conventional mainstream supermarkets have upped their game," Mackey said on a call with analysts in February. "We're going to do the best job that we can to keep our core customers from migrating back over to those guys."